On Tue, 2007-08-14 at 21:26 -0500, Dirk Eddelbuettel wrote:
Hi Dirk,
> UseR! 2007 at Iowa State University, Ames, IA, August 8-10, 2007
[...]
> II. Paper / presentation on 2000 new Debian packages --
> "Would you like 2000 new Debian packages with that?"
> ========================================================
>
> Something we hadn't really reported back to Debian is the relative success
> and current status of the 'pkg-bioc' project at Alioth.
[...]
> The big news is that we can now build most of the around two thousand source
> packages [ around 900 from CRAN and 1100 from BioC, I concentrate more on
> CRAN; Steffen focusses more on BioC, and David does everything ] for R from
> the CRAN and BioConductor archives. That's what our paper that I presented
> was about, as well as an earlier presentation / paper Steffen gave two months
> ago in Italy [1].
[...]
> The big question is what to do with these 2000 packages. The process is
> still too manual and fragile to be called 'production class'. Eventually
> this should move somewhere -- either CRAN itself, or, less likely, be part of
> Debian. I do say less likely here because I don't hink that two-thousand
> machine-generated packages could reach the Debian QA standards. They are
> also, as a large class, too esoteric. CRAN, on the other hand, builds
> binaries for Windows, so this could be a better fit. Someone suggested
> R-Forge -- which is a rather recent 'SF / Alioth for R' based on Debian's
> gforge packages. Also, one question had to do with how to avoid 'waits' for
> new packages -- people wouldn't want to wait for packages to reach testing
> when this can take months. So a distinct backport service may be the best
> option. Manpower and mirrors may be the crux.
First of all I really like your efforts of debianizing R packages. I
think debian is currently well suited to be used in ``science'' but yes
there is a lot more one can do. I was indeed missing the nowadays quite
standard bioconductor packages when I had to do some microarray
analysis.
Regarding machine generated debian packages it is a first step and
probably the only way given this amount of R-packages. I also don't
think they could be in debian. This especially holds for the more
esoteric/brand new research/unstable R-packes. However I would want to
see the more mature bioconductor packages in debian...
Thinking about it, *I* think it would be best to proceed in a similar
way as the texlive people, i.e. have debian packages for all major
categories which include the major mature R-packages of that category
r-bioc-base
r-bioc-microarray
r-bioc-annotation
r-bioc-statistics
r-bioc-graphs
r-bioc-technology
The remaining R-packages could be packaged as single debian-packages as
you proposed to do it and maybe even hosted a bioconductor.org? In case
a package seems more mature it can enter any of the categories and one
could add proper conflicts/replaces as an upgrade path. BTW, this also
solves the `not-up-to-date issue', as more mature packages don't require
weekly/monthly updates.
Soeren
--
For the one fact about the future of which we can be certain is that it
will be utterly fantastic. -- Arthur C. Clarke, 1962

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